A single SNP in an evolutionary conserved region within intron 86 of the HERC2 gene determines human blue-brown eye color

Abstract

We have previously demonstrated that haplotypes of three single nucleotide polymorphisms (SNPs) within the first intron of the OCA2 gene are extremely strongly associated with variation in human eye color. In the present work, we describe additional fine association mapping of eye color SNPs in the intergenic region upstream of OCA2 and within the neighboring HERC2 (hect domain and RLD2) gene. We screened an additional 92 SNPs in 300-3000 European individuals and found that a single SNP in intron 86 of HERC2, rs12913832, predicted eye color significantly better (ordinal logistic regression R(2) = 0.68, association LOD = 444) than our previous best OCA2 haplotype. Comparison of sequence alignments of multiple species showed that this SNP lies in the center of a short highly conserved sequence and that the blue-eye-associated allele (frequency 78%) breaks up this conserved sequence, part of which forms a consensus binding site for the helicase-like transcription factor (HLTF). We were also able to demonstrate the OCA2 R419Q, rs1800407, coding SNP acts as a penetrance modifier of this new HERC2 SNP for eye color, and somewhat independently, of melanoma risk. We conclude that the conserved region around rs12913832 represents a regulatory region controlling constitutive expression of OCA2 and that the C allele at rs12913832 leads to decreased expression of OCA2, particularly within iris melanocytes, which we postulate to be the ultimate cause of blue eye color.

Figure 1

Association of OCA2 and HERC2 SNPs with Eye Color Association of OCA2 and HERC2 SNPs with eye color (three-point scale) measured as R² in ordinal logistic regression analysis in the lower panel. The upper panel shows the linkage disequilibrium (r²) between the SNPs.

Figure 2

SNP Haplotypes Associated with Eye Color SNP haplotypes associated with blue and nonblue eye color spanning rs11855019 to rs1667394 of the OCA2-HERC2 locus. The SNP bases associated with blue and brown haplotypes are indicated by color.

Figure 3

Conserved Sequences in HERC Intron 86 (A) Dot-matrix-aligned sequence comparison of intron 86 from human HERC2 (x axis) and mouse Herc2 (y axis) with the MacVector program (MacVector, Inc.). (B) ClustalW alignment of the sequence similarity found in (A) with the RefSeq and Celera human with the RefSeq mouse sequences. Transcription factor binding sites identified by the MatInspector Program are boxed with SNP changes shown in color. (C) UCSC Genome Browser screen shot showing sequence alignment for seven species and associated phastCONS scores for sequence around rs12913832 of HERC2 intron 86. Sequence is shown in the 3′ to 5′ direction of the upper strand.